On Feb 7, 2011, at 9:57 AM, Andy Jenkinson wrote: > Might we add on to the end/beginning of GI instead of running concurrently > (assuming CSHL can oblige)?
David Stewart is pretty open to this kind of thing given enough forewarning. > Perhaps we can consider running a workshop at ISMB next year (California?) > should interest be sufficient for an event at GI or the like this year? ISMB is in California next year? Didn't know that. 2012 is far away though. > > I just noticed GI is actually in November though, by the way. There is also biology of genomes in May. > > On 7 Feb 2011, at 16:58, David Nix wrote: > >> Hmm... >> >> There's the Genome Informatics meeting in August at CSHL ( >> http://meetings.cshl.edu/meetings/info11.shtml). It's not the bay area and >> the organizers might already have a set program. There is a "Databases, >> Data Mining, Visualization and Curation" session by Alex Bateman and Ting >> Wang though. >> >> -cheers, D >> >> >> >> >> On 2/7/11 9:25 AM, "Ann Loraine" <[email protected]> wrote: >> >> Hi, >> >> Same for us here at UNC Charlotte. >> >> Meetings I'm attending next include two major plant science meetings >> (Arabidopsis and ASPB) and possibly ISMB in Vienna. >> >> David are there any other meetings you and your group are planning to >> attend? >> >> The ideal setting would be a meeting where we can do outreach and hold >> workshop event(s) for users, but also have a developers meeting where we >> discuss future directions for the software, DAS spec, etc. >> >> Are there other meetings that would be a good fit? >> >> Best, >> >> Ann >> >> On 2/7/11 10:58 AM, "David Nix" <[email protected]> wrote: >> >>> Ah, that makes sense. >>> >>> As for a US meeting, there are 3 or 4 folks here at the U of Utah that would >>> attend an out of state meeting. The bay area would be ideal (thanks Suzi!). >>> It might be best to make this part of a larger genomics/ proteomics meeting >>> to >>> start. This would draw more folks who are interested in distributing their >>> own data and working DAS access into their own applications. Are their any >>> appropriate upcoming meetings? >>> >>> -cheers, D >>> >>> >>> On 2/4/11 1:57 PM, "Andy Jenkinson" <[email protected]> wrote: >>> >>> Hi David, >>> >>> I guess one of the big reasons to want a proxy is it allows you to use DAS >>> sources you don't control, which is obviously potentially a really big >>> benefit >>> with so many DAS/1 sources around. I don't know if this is what Jim is >>> trying >>> to achieve though. In truth this has always been the difficulty with the >>> das/das2 tech divide really, with such a huge existing implementation base >>> there's a very high "activation energy" in switching! >>> >>> What was the issue with the ensembl servers? >>> >>> Jon and I have talked a few times about organising a DAS workshop in North >>> America, we just need someone to host (and to an extent fund) it. Do you >>> have >>> any suggestions? Almost all of the attendees for our workshops are from >>> Europe, in fact lots are from Hinxton. So what sort of demand do you think >>> there would be stateside for such an event? Enough for a standalone >>> workshop, >>> or more conducive to an add-on to or collaboration with another event? >>> >>> Maybe we can look into webcasting the talks? No idea how to go about this >>> though! >>> >>> On 4 Feb 2011, at 19:13, David Nix wrote: >>> >>>> Hello Jim, >>>> >>>> If I make a suggestion. If you're looking to visualize genomic data in >>>> IGB, >>>> it would be best to use a DAS/2 server such as the Classic (command line) >>>> or >>>> GenoPub (web app/ relational database) GenoViz DAS/2 server. DAS/2 is well >>>> suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, >>>> bar, >>>> useq...) and alignment data (ie BAM) to client apps. We're continuing to >>>> develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so >>>> expect continuing improvements (bulk uploading and file conversion, >>>> annotation via ontologies, super group visibility settings, additional file >>>> formats, etc.). See >>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2 and our >>>> paper >>>> http://www.biomedcentral.com/1471-2105/11/455 >>>> >>>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2 >>>> server supports DAS xml datasets so moving data from a DAS/1 server to >>>> DAS/2 >>>> wouldn't require any data reformatting. Although for large datasets, it's >>>> best to use one of the compressed binary data formats such as bar, bam, or >>>> useq. >>>> >>>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers. This >>>> works >>>> well for accessing their small annotation datasets (gene models: refseq, >>>> knowngenes), but the graph distribution wasn't functional the last I >>>> checked. >>>> The problem appeared to be from the server side. >>>> >>>> -cheers, David >>>> >>>> P.S. I wish I could attend the DAS workshop this year and show you what >>>> we've >>>> been up to. Any chance of getting a Skype conference call with posted >>>> presentations? Would be great if someone hosted a DAS Workshop in the US. >>>> >>>> >>>> On 2/4/11 8:19 AM, "Gregg Helt" <[email protected]> wrote: >>>> >>>> The core genomancer code is pretty stable, most of the recent work is >>>> in plugins (and some work in the core to allow more extensive >>>> plugins). >>>> >>>> You should be able to get a working DAS1-->DAS2 proxy running from >>>> the current head of the Trellis SVN repository -- you would just need >>>> to add a web.xml config file with servlet parameters to get it going in a >>>> servlet container like Tomcat, or alternatively run the built-in Jetty >>>> server >>>> (ExampleJettyDas2Server) and edit servlet parameters directly in code. >>>> >>>> But if the intent is to load DAS 1.x data into IGB, I don't think you >>>> need to use Trellis. Th latest IGB (6.4.1 loaded via WebStart) >>>> already supports DAS 1.5 access. In the "Data Access" tab, under >>>> "Choose Data Sources and Data Sets" section click the "Configure" >>>> button. This brings up a window with a "Data Sources" tab, and in >>>> that tab you can click the "Add" button to bring up a dialog that lets >>>> you select "DAS" for the data source type, and enter the URL for a DAS >>>> server. This worked fine for loading data from the UCSC DAS 1.5 >>>> server -- I haven't tried accessing data from any other DAS servers >>>> recently. >>>> >>>> I'm forwarding to the genoviz-devel list for IGB developments and >>>> discussion, to see if anyone currently working on IGB can add any more >>>> info. >>>> >>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter >>>> <[email protected]> wrote: >>>>> >>>>> Hi all (but Gregg in particular!) >>>>> >>>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy >>>>> in the Genomancer project (http://code.google.com/p/genomancer/) is >>>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and >>>>> it looks like there's a moderate amount of commit activity in the >>>>> project at the moment, making me a little nervous about attempting to >>>>> use the code in a production(ish) setting. >>>>> >>>>> many thanks in advance, >>>>> Jim. >>>>> >>>>> -- >>>>> ------------------------------------------------------------------- >>>>> J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group >>>>> Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk >>>>> The University of Dundee is a Scottish Registered Charity, No. SC015096. >>>>> >>>>> _______________________________________________ >>>>> DAS mailing list >>>>> [email protected] >>>>> http://lists.open-bio.org/mailman/listinfo/das >>>>> >>>> >>>> _______________________________________________ >>>> DAS mailing list >>>> [email protected] >>>> http://lists.open-bio.org/mailman/listinfo/das >>>> >>>> >>>> _______________________________________________ >>>> DAS mailing list >>>> [email protected] >>>> http://lists.open-bio.org/mailman/listinfo/das >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> The modern datacenter depends on network connectivity to access resources >>> and provide services. The best practices for maximizing a physical server's >>> connectivity to a physical network are well understood - see how these >>> rules translate into the virtual world? >>> http://p.sf.net/sfu/oracle-sfdevnlfb >>> _______________________________________________ >>> Genoviz-devel mailing list >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel >> >> -- >> Ann Loraine >> Associate Professor >> Dept. of Bioinformatics and Genomics, UNCC >> North Carolina Research Campus >> 600 Laureate Way >> Kannapolis, NC 28081 >> 704-250-5750 >> www.transvar.org >> >> >> > > > _______________________________________________ > DAS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/das _______________________________________________ DAS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/das
